Starting phenix.real_space_refine on Sat Mar 7 00:01:54 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7lmy_23442/03_2026/7lmy_23442.cif Found real_map, /net/cci-nas-00/data/ceres_data/7lmy_23442/03_2026/7lmy_23442.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7lmy_23442/03_2026/7lmy_23442.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7lmy_23442/03_2026/7lmy_23442.map" model { file = "/net/cci-nas-00/data/ceres_data/7lmy_23442/03_2026/7lmy_23442.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7lmy_23442/03_2026/7lmy_23442.cif" } resolution = 2.4 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.003 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians P 36 5.49 5 Mg 12 5.21 5 S 192 5.16 5 C 22338 2.51 5 N 6300 2.21 5 O 6768 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 60 residue(s): 0.04s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 35646 Number of models: 1 Model: "" Number of chains: 12 Chain: "A" Number of atoms: 5841 Number of conformers: 1 Conformer: "" Number of residues, atoms: 745, 5841 Classifications: {'peptide': 745} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PCIS': 4, 'PTRANS': 37, 'TRANS': 703} Chain breaks: 2 Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 15 Unresolved non-hydrogen dihedrals: 9 Planarities with less than four sites: {'GLU:plan': 2, 'GLN:plan1': 1} Unresolved non-hydrogen planarities: 12 Chain: "B" Number of atoms: 5841 Number of conformers: 1 Conformer: "" Number of residues, atoms: 745, 5841 Classifications: {'peptide': 745} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PCIS': 4, 'PTRANS': 37, 'TRANS': 703} Chain breaks: 2 Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 15 Unresolved non-hydrogen dihedrals: 9 Planarities with less than four sites: {'GLU:plan': 2, 'GLN:plan1': 1} Unresolved non-hydrogen planarities: 12 Chain: "C" Number of atoms: 5841 Number of conformers: 1 Conformer: "" Number of residues, atoms: 745, 5841 Classifications: {'peptide': 745} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PCIS': 4, 'PTRANS': 37, 'TRANS': 703} Chain breaks: 2 Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 15 Unresolved non-hydrogen dihedrals: 9 Planarities with less than four sites: {'GLU:plan': 2, 'GLN:plan1': 1} Unresolved non-hydrogen planarities: 12 Chain: "D" Number of atoms: 5841 Number of conformers: 1 Conformer: "" Number of residues, atoms: 745, 5841 Classifications: {'peptide': 745} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PCIS': 4, 'PTRANS': 37, 'TRANS': 703} Chain breaks: 2 Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 15 Unresolved non-hydrogen dihedrals: 9 Planarities with less than four sites: {'GLU:plan': 2, 'GLN:plan1': 1} Unresolved non-hydrogen planarities: 12 Chain: "E" Number of atoms: 5841 Number of conformers: 1 Conformer: "" Number of residues, atoms: 745, 5841 Classifications: {'peptide': 745} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PCIS': 4, 'PTRANS': 37, 'TRANS': 703} Chain breaks: 2 Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 15 Unresolved non-hydrogen dihedrals: 9 Planarities with less than four sites: {'GLU:plan': 2, 'GLN:plan1': 1} Unresolved non-hydrogen planarities: 12 Chain: "F" Number of atoms: 5841 Number of conformers: 1 Conformer: "" Number of residues, atoms: 745, 5841 Classifications: {'peptide': 745} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PCIS': 4, 'PTRANS': 37, 'TRANS': 703} Chain breaks: 2 Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 15 Unresolved non-hydrogen dihedrals: 9 Planarities with less than four sites: {'GLU:plan': 2, 'GLN:plan1': 1} Unresolved non-hydrogen planarities: 12 Chain: "A" Number of atoms: 100 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 100 Unusual residues: {' MG': 2, 'ATP': 2, 'Y6Y': 1} Classifications: {'undetermined': 5} Link IDs: {None: 4} Chain: "B" Number of atoms: 100 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 100 Unusual residues: {' MG': 2, 'ATP': 2, 'Y6Y': 1} Classifications: {'undetermined': 5} Link IDs: {None: 4} Chain: "C" Number of atoms: 100 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 100 Unusual residues: {' MG': 2, 'ATP': 2, 'Y6Y': 1} Classifications: {'undetermined': 5} Link IDs: {None: 4} Chain: "D" Number of atoms: 100 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 100 Unusual residues: {' MG': 2, 'ATP': 2, 'Y6Y': 1} Classifications: {'undetermined': 5} Link IDs: {None: 4} Chain: "E" Number of atoms: 100 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 100 Unusual residues: {' MG': 2, 'ATP': 2, 'Y6Y': 1} Classifications: {'undetermined': 5} Link IDs: {None: 4} Chain: "F" Number of atoms: 100 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 100 Unusual residues: {' MG': 2, 'ATP': 2, 'Y6Y': 1} Classifications: {'undetermined': 5} Link IDs: {None: 4} Time building chain proxies: 7.86, per 1000 atoms: 0.22 Number of scatterers: 35646 At special positions: 0 Unit cell: (175.395, 169.017, 113.741, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 192 16.00 P 36 15.00 Mg 12 11.99 O 6768 8.00 N 6300 7.00 C 22338 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.81 Conformation dependent library (CDL) restraints added in 1.6 seconds 8868 Ramachandran restraints generated. 4434 Oldfield, 0 Emsley, 4434 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 8364 Finding SS restraints... Secondary structure from input PDB file: 234 helices and 30 sheets defined 53.8% alpha, 13.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.15 Creating SS restraints... Processing helix chain 'A' and resid 14 through 18 Processing helix chain 'A' and resid 42 through 50 Processing helix chain 'A' and resid 85 through 92 Processing helix chain 'A' and resid 119 through 124 Processing helix chain 'A' and resid 129 through 134 Processing helix chain 'A' and resid 134 through 139 Processing helix chain 'A' and resid 190 through 199 removed outlier: 3.525A pdb=" N GLU A 194 " --> pdb=" O LYS A 190 " (cutoff:3.500A) Processing helix chain 'A' and resid 202 through 206 Processing helix chain 'A' and resid 209 through 220 Processing helix chain 'A' and resid 220 through 226 removed outlier: 3.613A pdb=" N LEU A 224 " --> pdb=" O VAL A 220 " (cutoff:3.500A) Processing helix chain 'A' and resid 226 through 233 removed outlier: 3.911A pdb=" N PHE A 230 " --> pdb=" O HIS A 226 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N ILE A 233 " --> pdb=" O LEU A 229 " (cutoff:3.500A) Processing helix chain 'A' and resid 250 through 262 Processing helix chain 'A' and resid 271 through 276 Processing helix chain 'A' and resid 280 through 296 removed outlier: 3.557A pdb=" N SER A 284 " --> pdb=" O GLY A 280 " (cutoff:3.500A) Processing helix chain 'A' and resid 305 through 310 removed outlier: 4.071A pdb=" N ILE A 309 " --> pdb=" O GLU A 305 " (cutoff:3.500A) Processing helix chain 'A' and resid 318 through 335 removed outlier: 3.777A pdb=" N LEU A 335 " --> pdb=" O LEU A 331 " (cutoff:3.500A) Processing helix chain 'A' and resid 349 through 353 Processing helix chain 'A' and resid 354 through 359 Processing helix chain 'A' and resid 373 through 385 Processing helix chain 'A' and resid 395 through 403 Processing helix chain 'A' and resid 407 through 425 Processing helix chain 'A' and resid 426 through 430 Processing helix chain 'A' and resid 438 through 445 Processing helix chain 'A' and resid 448 through 459 Processing helix chain 'A' and resid 475 through 479 Processing helix chain 'A' and resid 482 through 499 Proline residue: A 496 - end of helix Processing helix chain 'A' and resid 499 through 507 removed outlier: 3.745A pdb=" N PHE A 503 " --> pdb=" O HIS A 499 " (cutoff:3.500A) Processing helix chain 'A' and resid 523 through 535 removed outlier: 3.529A pdb=" N CYS A 535 " --> pdb=" O ILE A 531 " (cutoff:3.500A) Processing helix chain 'A' and resid 543 through 553 Processing helix chain 'A' and resid 557 through 569 removed outlier: 4.020A pdb=" N GLU A 561 " --> pdb=" O ALA A 557 " (cutoff:3.500A) Processing helix chain 'A' and resid 580 through 586 Processing helix chain 'A' and resid 598 through 612 Processing helix chain 'A' and resid 625 through 629 Processing helix chain 'A' and resid 630 through 635 removed outlier: 3.506A pdb=" N ARG A 635 " --> pdb=" O ALA A 632 " (cutoff:3.500A) Processing helix chain 'A' and resid 649 through 661 Processing helix chain 'A' and resid 671 through 679 Processing helix chain 'A' and resid 683 through 714 removed outlier: 3.816A pdb=" N GLN A 714 " --> pdb=" O GLU A 710 " (cutoff:3.500A) Processing helix chain 'A' and resid 732 through 743 removed outlier: 4.191A pdb=" N PHE A 742 " --> pdb=" O GLU A 738 " (cutoff:3.500A) Processing helix chain 'A' and resid 748 through 761 Processing helix chain 'B' and resid 14 through 18 Processing helix chain 'B' and resid 42 through 50 Processing helix chain 'B' and resid 85 through 92 Processing helix chain 'B' and resid 119 through 124 Processing helix chain 'B' and resid 129 through 134 Processing helix chain 'B' and resid 134 through 139 Processing helix chain 'B' and resid 190 through 199 removed outlier: 3.525A pdb=" N GLU B 194 " --> pdb=" O LYS B 190 " (cutoff:3.500A) Processing helix chain 'B' and resid 202 through 206 Processing helix chain 'B' and resid 209 through 220 Processing helix chain 'B' and resid 220 through 226 removed outlier: 3.613A pdb=" N LEU B 224 " --> pdb=" O VAL B 220 " (cutoff:3.500A) Processing helix chain 'B' and resid 226 through 233 removed outlier: 3.911A pdb=" N PHE B 230 " --> pdb=" O HIS B 226 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N ILE B 233 " --> pdb=" O LEU B 229 " (cutoff:3.500A) Processing helix chain 'B' and resid 250 through 262 Processing helix chain 'B' and resid 271 through 276 Processing helix chain 'B' and resid 280 through 296 removed outlier: 3.557A pdb=" N SER B 284 " --> pdb=" O GLY B 280 " (cutoff:3.500A) Processing helix chain 'B' and resid 305 through 310 removed outlier: 4.071A pdb=" N ILE B 309 " --> pdb=" O GLU B 305 " (cutoff:3.500A) Processing helix chain 'B' and resid 318 through 335 removed outlier: 3.777A pdb=" N LEU B 335 " --> pdb=" O LEU B 331 " (cutoff:3.500A) Processing helix chain 'B' and resid 349 through 353 Processing helix chain 'B' and resid 354 through 359 Processing helix chain 'B' and resid 373 through 385 Processing helix chain 'B' and resid 395 through 403 Processing helix chain 'B' and resid 407 through 426 removed outlier: 3.512A pdb=" N LYS B 426 " --> pdb=" O ALA B 422 " (cutoff:3.500A) Processing helix chain 'B' and resid 427 through 430 Processing helix chain 'B' and resid 438 through 445 Processing helix chain 'B' and resid 448 through 459 Processing helix chain 'B' and resid 475 through 479 Processing helix chain 'B' and resid 482 through 499 Proline residue: B 496 - end of helix Processing helix chain 'B' and resid 499 through 507 removed outlier: 3.744A pdb=" N PHE B 503 " --> pdb=" O HIS B 499 " (cutoff:3.500A) Processing helix chain 'B' and resid 523 through 535 removed outlier: 3.529A pdb=" N CYS B 535 " --> pdb=" O ILE B 531 " (cutoff:3.500A) Processing helix chain 'B' and resid 543 through 553 Processing helix chain 'B' and resid 557 through 569 removed outlier: 4.021A pdb=" N GLU B 561 " --> pdb=" O ALA B 557 " (cutoff:3.500A) Processing helix chain 'B' and resid 580 through 586 Processing helix chain 'B' and resid 598 through 612 Processing helix chain 'B' and resid 625 through 629 Processing helix chain 'B' and resid 630 through 635 removed outlier: 3.506A pdb=" N ARG B 635 " --> pdb=" O ALA B 632 " (cutoff:3.500A) Processing helix chain 'B' and resid 649 through 661 Processing helix chain 'B' and resid 671 through 679 Processing helix chain 'B' and resid 683 through 714 removed outlier: 3.816A pdb=" N GLN B 714 " --> pdb=" O GLU B 710 " (cutoff:3.500A) Processing helix chain 'B' and resid 732 through 743 removed outlier: 4.190A pdb=" N PHE B 742 " --> pdb=" O GLU B 738 " (cutoff:3.500A) Processing helix chain 'B' and resid 748 through 761 Processing helix chain 'C' and resid 14 through 18 Processing helix chain 'C' and resid 42 through 50 Processing helix chain 'C' and resid 85 through 92 Processing helix chain 'C' and resid 119 through 124 Processing helix chain 'C' and resid 129 through 134 Processing helix chain 'C' and resid 134 through 139 Processing helix chain 'C' and resid 190 through 199 removed outlier: 3.526A pdb=" N GLU C 194 " --> pdb=" O LYS C 190 " (cutoff:3.500A) Processing helix chain 'C' and resid 202 through 206 Processing helix chain 'C' and resid 209 through 220 Processing helix chain 'C' and resid 220 through 226 removed outlier: 3.613A pdb=" N LEU C 224 " --> pdb=" O VAL C 220 " (cutoff:3.500A) Processing helix chain 'C' and resid 226 through 233 removed outlier: 3.910A pdb=" N PHE C 230 " --> pdb=" O HIS C 226 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N ILE C 233 " --> pdb=" O LEU C 229 " (cutoff:3.500A) Processing helix chain 'C' and resid 250 through 262 Processing helix chain 'C' and resid 271 through 276 Processing helix chain 'C' and resid 280 through 296 removed outlier: 3.558A pdb=" N SER C 284 " --> pdb=" O GLY C 280 " (cutoff:3.500A) Processing helix chain 'C' and resid 305 through 310 removed outlier: 4.072A pdb=" N ILE C 309 " --> pdb=" O GLU C 305 " (cutoff:3.500A) Processing helix chain 'C' and resid 318 through 335 removed outlier: 3.777A pdb=" N LEU C 335 " --> pdb=" O LEU C 331 " (cutoff:3.500A) Processing helix chain 'C' and resid 349 through 353 Processing helix chain 'C' and resid 354 through 359 Processing helix chain 'C' and resid 373 through 385 Processing helix chain 'C' and resid 395 through 403 Processing helix chain 'C' and resid 407 through 425 Processing helix chain 'C' and resid 426 through 430 Processing helix chain 'C' and resid 438 through 445 Processing helix chain 'C' and resid 448 through 459 Processing helix chain 'C' and resid 475 through 479 Processing helix chain 'C' and resid 482 through 499 Proline residue: C 496 - end of helix Processing helix chain 'C' and resid 499 through 507 removed outlier: 3.745A pdb=" N PHE C 503 " --> pdb=" O HIS C 499 " (cutoff:3.500A) Processing helix chain 'C' and resid 523 through 535 removed outlier: 3.530A pdb=" N CYS C 535 " --> pdb=" O ILE C 531 " (cutoff:3.500A) Processing helix chain 'C' and resid 543 through 553 Processing helix chain 'C' and resid 557 through 569 removed outlier: 4.021A pdb=" N GLU C 561 " --> pdb=" O ALA C 557 " (cutoff:3.500A) Processing helix chain 'C' and resid 580 through 586 Processing helix chain 'C' and resid 598 through 612 Processing helix chain 'C' and resid 625 through 629 Processing helix chain 'C' and resid 630 through 635 removed outlier: 3.506A pdb=" N ARG C 635 " --> pdb=" O ALA C 632 " (cutoff:3.500A) Processing helix chain 'C' and resid 649 through 661 Processing helix chain 'C' and resid 671 through 679 Processing helix chain 'C' and resid 683 through 714 removed outlier: 3.816A pdb=" N GLN C 714 " --> pdb=" O GLU C 710 " (cutoff:3.500A) Processing helix chain 'C' and resid 732 through 743 removed outlier: 4.190A pdb=" N PHE C 742 " --> pdb=" O GLU C 738 " (cutoff:3.500A) Processing helix chain 'C' and resid 748 through 761 Processing helix chain 'D' and resid 14 through 18 Processing helix chain 'D' and resid 42 through 50 Processing helix chain 'D' and resid 85 through 92 Processing helix chain 'D' and resid 119 through 124 Processing helix chain 'D' and resid 129 through 134 Processing helix chain 'D' and resid 134 through 139 Processing helix chain 'D' and resid 190 through 199 removed outlier: 3.526A pdb=" N GLU D 194 " --> pdb=" O LYS D 190 " (cutoff:3.500A) Processing helix chain 'D' and resid 202 through 206 Processing helix chain 'D' and resid 209 through 220 Processing helix chain 'D' and resid 220 through 226 removed outlier: 3.613A pdb=" N LEU D 224 " --> pdb=" O VAL D 220 " (cutoff:3.500A) Processing helix chain 'D' and resid 226 through 233 removed outlier: 3.910A pdb=" N PHE D 230 " --> pdb=" O HIS D 226 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N ILE D 233 " --> pdb=" O LEU D 229 " (cutoff:3.500A) Processing helix chain 'D' and resid 250 through 262 Processing helix chain 'D' and resid 271 through 276 Processing helix chain 'D' and resid 280 through 296 removed outlier: 3.557A pdb=" N SER D 284 " --> pdb=" O GLY D 280 " (cutoff:3.500A) Processing helix chain 'D' and resid 305 through 310 removed outlier: 4.073A pdb=" N ILE D 309 " --> pdb=" O GLU D 305 " (cutoff:3.500A) Processing helix chain 'D' and resid 318 through 335 removed outlier: 3.776A pdb=" N LEU D 335 " --> pdb=" O LEU D 331 " (cutoff:3.500A) Processing helix chain 'D' and resid 349 through 353 Processing helix chain 'D' and resid 354 through 359 Processing helix chain 'D' and resid 373 through 385 Processing helix chain 'D' and resid 395 through 403 Processing helix chain 'D' and resid 407 through 425 Processing helix chain 'D' and resid 426 through 430 Processing helix chain 'D' and resid 438 through 445 Processing helix chain 'D' and resid 448 through 459 Processing helix chain 'D' and resid 475 through 479 Processing helix chain 'D' and resid 482 through 499 Proline residue: D 496 - end of helix Processing helix chain 'D' and resid 499 through 507 removed outlier: 3.744A pdb=" N PHE D 503 " --> pdb=" O HIS D 499 " (cutoff:3.500A) Processing helix chain 'D' and resid 523 through 535 removed outlier: 3.530A pdb=" N CYS D 535 " --> pdb=" O ILE D 531 " (cutoff:3.500A) Processing helix chain 'D' and resid 543 through 553 Processing helix chain 'D' and resid 557 through 569 removed outlier: 4.021A pdb=" N GLU D 561 " --> pdb=" O ALA D 557 " (cutoff:3.500A) Processing helix chain 'D' and resid 580 through 586 Processing helix chain 'D' and resid 598 through 612 Processing helix chain 'D' and resid 625 through 629 Processing helix chain 'D' and resid 630 through 635 removed outlier: 3.506A pdb=" N ARG D 635 " --> pdb=" O ALA D 632 " (cutoff:3.500A) Processing helix chain 'D' and resid 649 through 661 Processing helix chain 'D' and resid 671 through 679 Processing helix chain 'D' and resid 683 through 714 removed outlier: 3.815A pdb=" N GLN D 714 " --> pdb=" O GLU D 710 " (cutoff:3.500A) Processing helix chain 'D' and resid 732 through 743 removed outlier: 4.190A pdb=" N PHE D 742 " --> pdb=" O GLU D 738 " (cutoff:3.500A) Processing helix chain 'D' and resid 748 through 761 Processing helix chain 'E' and resid 14 through 18 Processing helix chain 'E' and resid 42 through 50 Processing helix chain 'E' and resid 85 through 92 Processing helix chain 'E' and resid 119 through 124 Processing helix chain 'E' and resid 129 through 134 Processing helix chain 'E' and resid 134 through 139 Processing helix chain 'E' and resid 190 through 199 removed outlier: 3.525A pdb=" N GLU E 194 " --> pdb=" O LYS E 190 " (cutoff:3.500A) Processing helix chain 'E' and resid 202 through 206 Processing helix chain 'E' and resid 209 through 220 Processing helix chain 'E' and resid 220 through 226 removed outlier: 3.613A pdb=" N LEU E 224 " --> pdb=" O VAL E 220 " (cutoff:3.500A) Processing helix chain 'E' and resid 226 through 233 removed outlier: 3.911A pdb=" N PHE E 230 " --> pdb=" O HIS E 226 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N ILE E 233 " --> pdb=" O LEU E 229 " (cutoff:3.500A) Processing helix chain 'E' and resid 250 through 262 Processing helix chain 'E' and resid 271 through 276 Processing helix chain 'E' and resid 280 through 296 removed outlier: 3.557A pdb=" N SER E 284 " --> pdb=" O GLY E 280 " (cutoff:3.500A) Processing helix chain 'E' and resid 305 through 310 removed outlier: 4.072A pdb=" N ILE E 309 " --> pdb=" O GLU E 305 " (cutoff:3.500A) Processing helix chain 'E' and resid 318 through 335 removed outlier: 3.777A pdb=" N LEU E 335 " --> pdb=" O LEU E 331 " (cutoff:3.500A) Processing helix chain 'E' and resid 349 through 353 Processing helix chain 'E' and resid 354 through 359 Processing helix chain 'E' and resid 373 through 385 Processing helix chain 'E' and resid 395 through 403 Processing helix chain 'E' and resid 407 through 426 removed outlier: 3.511A pdb=" N LYS E 426 " --> pdb=" O ALA E 422 " (cutoff:3.500A) Processing helix chain 'E' and resid 427 through 430 Processing helix chain 'E' and resid 438 through 445 Processing helix chain 'E' and resid 448 through 459 Processing helix chain 'E' and resid 475 through 479 Processing helix chain 'E' and resid 482 through 499 Proline residue: E 496 - end of helix Processing helix chain 'E' and resid 499 through 507 removed outlier: 3.745A pdb=" N PHE E 503 " --> pdb=" O HIS E 499 " (cutoff:3.500A) Processing helix chain 'E' and resid 523 through 535 removed outlier: 3.530A pdb=" N CYS E 535 " --> pdb=" O ILE E 531 " (cutoff:3.500A) Processing helix chain 'E' and resid 543 through 553 Processing helix chain 'E' and resid 557 through 569 removed outlier: 4.020A pdb=" N GLU E 561 " --> pdb=" O ALA E 557 " (cutoff:3.500A) Processing helix chain 'E' and resid 580 through 586 Processing helix chain 'E' and resid 598 through 612 Processing helix chain 'E' and resid 625 through 629 Processing helix chain 'E' and resid 630 through 635 removed outlier: 3.507A pdb=" N ARG E 635 " --> pdb=" O ALA E 632 " (cutoff:3.500A) Processing helix chain 'E' and resid 649 through 661 Processing helix chain 'E' and resid 671 through 679 Processing helix chain 'E' and resid 683 through 714 removed outlier: 3.816A pdb=" N GLN E 714 " --> pdb=" O GLU E 710 " (cutoff:3.500A) Processing helix chain 'E' and resid 732 through 743 removed outlier: 4.190A pdb=" N PHE E 742 " --> pdb=" O GLU E 738 " (cutoff:3.500A) Processing helix chain 'E' and resid 748 through 761 Processing helix chain 'F' and resid 14 through 18 Processing helix chain 'F' and resid 42 through 50 Processing helix chain 'F' and resid 85 through 92 Processing helix chain 'F' and resid 119 through 124 Processing helix chain 'F' and resid 129 through 134 Processing helix chain 'F' and resid 134 through 139 Processing helix chain 'F' and resid 190 through 199 removed outlier: 3.526A pdb=" N GLU F 194 " --> pdb=" O LYS F 190 " (cutoff:3.500A) Processing helix chain 'F' and resid 202 through 206 Processing helix chain 'F' and resid 209 through 220 Processing helix chain 'F' and resid 220 through 226 removed outlier: 3.613A pdb=" N LEU F 224 " --> pdb=" O VAL F 220 " (cutoff:3.500A) Processing helix chain 'F' and resid 226 through 233 removed outlier: 3.911A pdb=" N PHE F 230 " --> pdb=" O HIS F 226 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N ILE F 233 " --> pdb=" O LEU F 229 " (cutoff:3.500A) Processing helix chain 'F' and resid 250 through 262 Processing helix chain 'F' and resid 271 through 276 Processing helix chain 'F' and resid 280 through 296 removed outlier: 3.557A pdb=" N SER F 284 " --> pdb=" O GLY F 280 " (cutoff:3.500A) Processing helix chain 'F' and resid 305 through 310 removed outlier: 4.072A pdb=" N ILE F 309 " --> pdb=" O GLU F 305 " (cutoff:3.500A) Processing helix chain 'F' and resid 318 through 335 removed outlier: 3.776A pdb=" N LEU F 335 " --> pdb=" O LEU F 331 " (cutoff:3.500A) Processing helix chain 'F' and resid 349 through 353 Processing helix chain 'F' and resid 354 through 359 Processing helix chain 'F' and resid 373 through 385 Processing helix chain 'F' and resid 395 through 403 Processing helix chain 'F' and resid 407 through 426 removed outlier: 3.512A pdb=" N LYS F 426 " --> pdb=" O ALA F 422 " (cutoff:3.500A) Processing helix chain 'F' and resid 427 through 430 Processing helix chain 'F' and resid 438 through 445 Processing helix chain 'F' and resid 448 through 459 Processing helix chain 'F' and resid 475 through 479 Processing helix chain 'F' and resid 482 through 499 Proline residue: F 496 - end of helix Processing helix chain 'F' and resid 499 through 507 removed outlier: 3.745A pdb=" N PHE F 503 " --> pdb=" O HIS F 499 " (cutoff:3.500A) Processing helix chain 'F' and resid 523 through 535 removed outlier: 3.530A pdb=" N CYS F 535 " --> pdb=" O ILE F 531 " (cutoff:3.500A) Processing helix chain 'F' and resid 543 through 553 Processing helix chain 'F' and resid 557 through 569 removed outlier: 4.021A pdb=" N GLU F 561 " --> pdb=" O ALA F 557 " (cutoff:3.500A) Processing helix chain 'F' and resid 580 through 586 Processing helix chain 'F' and resid 598 through 612 Processing helix chain 'F' and resid 625 through 629 Processing helix chain 'F' and resid 630 through 635 removed outlier: 3.506A pdb=" N ARG F 635 " --> pdb=" O ALA F 632 " (cutoff:3.500A) Processing helix chain 'F' and resid 649 through 661 Processing helix chain 'F' and resid 671 through 679 Processing helix chain 'F' and resid 683 through 714 removed outlier: 3.816A pdb=" N GLN F 714 " --> pdb=" O GLU F 710 " (cutoff:3.500A) Processing helix chain 'F' and resid 732 through 743 removed outlier: 4.190A pdb=" N PHE F 742 " --> pdb=" O GLU F 738 " (cutoff:3.500A) Processing helix chain 'F' and resid 748 through 761 Processing sheet with id=AA1, first strand: chain 'A' and resid 25 through 30 removed outlier: 7.478A pdb=" N ILE A 82 " --> pdb=" O ARG A 25 " (cutoff:3.500A) removed outlier: 6.203A pdb=" N ILE A 27 " --> pdb=" O ILE A 82 " (cutoff:3.500A) removed outlier: 7.182A pdb=" N MET A 84 " --> pdb=" O ILE A 27 " (cutoff:3.500A) removed outlier: 5.568A pdb=" N ASP A 29 " --> pdb=" O MET A 84 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 151 through 154 removed outlier: 6.472A pdb=" N HIS A 115 " --> pdb=" O VAL A 166 " (cutoff:3.500A) removed outlier: 4.486A pdb=" N THR A 168 " --> pdb=" O ARG A 113 " (cutoff:3.500A) removed outlier: 6.597A pdb=" N ARG A 113 " --> pdb=" O THR A 168 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 145 through 147 Processing sheet with id=AA4, first strand: chain 'A' and resid 265 through 270 removed outlier: 6.600A pdb=" N ALA A 299 " --> pdb=" O ILE A 342 " (cutoff:3.500A) removed outlier: 7.623A pdb=" N MET A 344 " --> pdb=" O ALA A 299 " (cutoff:3.500A) removed outlier: 5.937A pdb=" N ILE A 301 " --> pdb=" O MET A 344 " (cutoff:3.500A) removed outlier: 7.744A pdb=" N ALA A 346 " --> pdb=" O ILE A 301 " (cutoff:3.500A) removed outlier: 6.774A pdb=" N ILE A 303 " --> pdb=" O ALA A 346 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 538 through 542 removed outlier: 6.574A pdb=" N ASN A 538 " --> pdb=" O VAL A 573 " (cutoff:3.500A) removed outlier: 7.442A pdb=" N PHE A 575 " --> pdb=" O ASN A 538 " (cutoff:3.500A) removed outlier: 6.284A pdb=" N ILE A 540 " --> pdb=" O PHE A 575 " (cutoff:3.500A) removed outlier: 6.475A pdb=" N CYS A 572 " --> pdb=" O PHE A 618 " (cutoff:3.500A) removed outlier: 7.674A pdb=" N ILE A 620 " --> pdb=" O CYS A 572 " (cutoff:3.500A) removed outlier: 6.135A pdb=" N LEU A 574 " --> pdb=" O ILE A 620 " (cutoff:3.500A) removed outlier: 7.772A pdb=" N ALA A 622 " --> pdb=" O LEU A 574 " (cutoff:3.500A) removed outlier: 6.590A pdb=" N PHE A 576 " --> pdb=" O ALA A 622 " (cutoff:3.500A) removed outlier: 6.839A pdb=" N GLY A 513 " --> pdb=" O GLN A 641 " (cutoff:3.500A) removed outlier: 7.895A pdb=" N ILE A 643 " --> pdb=" O GLY A 513 " (cutoff:3.500A) removed outlier: 6.250A pdb=" N LEU A 515 " --> pdb=" O ILE A 643 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 25 through 30 removed outlier: 7.478A pdb=" N ILE B 82 " --> pdb=" O ARG B 25 " (cutoff:3.500A) removed outlier: 6.203A pdb=" N ILE B 27 " --> pdb=" O ILE B 82 " (cutoff:3.500A) removed outlier: 7.183A pdb=" N MET B 84 " --> pdb=" O ILE B 27 " (cutoff:3.500A) removed outlier: 5.568A pdb=" N ASP B 29 " --> pdb=" O MET B 84 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 151 through 154 removed outlier: 6.470A pdb=" N HIS B 115 " --> pdb=" O VAL B 166 " (cutoff:3.500A) removed outlier: 4.486A pdb=" N THR B 168 " --> pdb=" O ARG B 113 " (cutoff:3.500A) removed outlier: 6.597A pdb=" N ARG B 113 " --> pdb=" O THR B 168 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 145 through 147 Processing sheet with id=AA9, first strand: chain 'B' and resid 265 through 270 removed outlier: 6.599A pdb=" N ALA B 299 " --> pdb=" O ILE B 342 " (cutoff:3.500A) removed outlier: 7.623A pdb=" N MET B 344 " --> pdb=" O ALA B 299 " (cutoff:3.500A) removed outlier: 5.937A pdb=" N ILE B 301 " --> pdb=" O MET B 344 " (cutoff:3.500A) removed outlier: 7.744A pdb=" N ALA B 346 " --> pdb=" O ILE B 301 " (cutoff:3.500A) removed outlier: 6.773A pdb=" N ILE B 303 " --> pdb=" O ALA B 346 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 538 through 542 removed outlier: 6.574A pdb=" N ASN B 538 " --> pdb=" O VAL B 573 " (cutoff:3.500A) removed outlier: 7.443A pdb=" N PHE B 575 " --> pdb=" O ASN B 538 " (cutoff:3.500A) removed outlier: 6.285A pdb=" N ILE B 540 " --> pdb=" O PHE B 575 " (cutoff:3.500A) removed outlier: 6.475A pdb=" N CYS B 572 " --> pdb=" O PHE B 618 " (cutoff:3.500A) removed outlier: 7.673A pdb=" N ILE B 620 " --> pdb=" O CYS B 572 " (cutoff:3.500A) removed outlier: 6.135A pdb=" N LEU B 574 " --> pdb=" O ILE B 620 " (cutoff:3.500A) removed outlier: 7.771A pdb=" N ALA B 622 " --> pdb=" O LEU B 574 " (cutoff:3.500A) removed outlier: 6.590A pdb=" N PHE B 576 " --> pdb=" O ALA B 622 " (cutoff:3.500A) removed outlier: 6.839A pdb=" N GLY B 513 " --> pdb=" O GLN B 641 " (cutoff:3.500A) removed outlier: 7.895A pdb=" N ILE B 643 " --> pdb=" O GLY B 513 " (cutoff:3.500A) removed outlier: 6.250A pdb=" N LEU B 515 " --> pdb=" O ILE B 643 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 25 through 30 removed outlier: 7.478A pdb=" N ILE C 82 " --> pdb=" O ARG C 25 " (cutoff:3.500A) removed outlier: 6.203A pdb=" N ILE C 27 " --> pdb=" O ILE C 82 " (cutoff:3.500A) removed outlier: 7.183A pdb=" N MET C 84 " --> pdb=" O ILE C 27 " (cutoff:3.500A) removed outlier: 5.569A pdb=" N ASP C 29 " --> pdb=" O MET C 84 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 151 through 154 removed outlier: 6.471A pdb=" N HIS C 115 " --> pdb=" O VAL C 166 " (cutoff:3.500A) removed outlier: 4.486A pdb=" N THR C 168 " --> pdb=" O ARG C 113 " (cutoff:3.500A) removed outlier: 6.596A pdb=" N ARG C 113 " --> pdb=" O THR C 168 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'C' and resid 145 through 147 Processing sheet with id=AB5, first strand: chain 'C' and resid 265 through 270 removed outlier: 6.599A pdb=" N ALA C 299 " --> pdb=" O ILE C 342 " (cutoff:3.500A) removed outlier: 7.624A pdb=" N MET C 344 " --> pdb=" O ALA C 299 " (cutoff:3.500A) removed outlier: 5.937A pdb=" N ILE C 301 " --> pdb=" O MET C 344 " (cutoff:3.500A) removed outlier: 7.744A pdb=" N ALA C 346 " --> pdb=" O ILE C 301 " (cutoff:3.500A) removed outlier: 6.774A pdb=" N ILE C 303 " --> pdb=" O ALA C 346 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'C' and resid 538 through 542 removed outlier: 6.574A pdb=" N ASN C 538 " --> pdb=" O VAL C 573 " (cutoff:3.500A) removed outlier: 7.443A pdb=" N PHE C 575 " --> pdb=" O ASN C 538 " (cutoff:3.500A) removed outlier: 6.284A pdb=" N ILE C 540 " --> pdb=" O PHE C 575 " (cutoff:3.500A) removed outlier: 6.474A pdb=" N CYS C 572 " --> pdb=" O PHE C 618 " (cutoff:3.500A) removed outlier: 7.673A pdb=" N ILE C 620 " --> pdb=" O CYS C 572 " (cutoff:3.500A) removed outlier: 6.136A pdb=" N LEU C 574 " --> pdb=" O ILE C 620 " (cutoff:3.500A) removed outlier: 7.771A pdb=" N ALA C 622 " --> pdb=" O LEU C 574 " (cutoff:3.500A) removed outlier: 6.589A pdb=" N PHE C 576 " --> pdb=" O ALA C 622 " (cutoff:3.500A) removed outlier: 6.839A pdb=" N GLY C 513 " --> pdb=" O GLN C 641 " (cutoff:3.500A) removed outlier: 7.895A pdb=" N ILE C 643 " --> pdb=" O GLY C 513 " (cutoff:3.500A) removed outlier: 6.250A pdb=" N LEU C 515 " --> pdb=" O ILE C 643 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'D' and resid 25 through 30 removed outlier: 7.479A pdb=" N ILE D 82 " --> pdb=" O ARG D 25 " (cutoff:3.500A) removed outlier: 6.203A pdb=" N ILE D 27 " --> pdb=" O ILE D 82 " (cutoff:3.500A) removed outlier: 7.182A pdb=" N MET D 84 " --> pdb=" O ILE D 27 " (cutoff:3.500A) removed outlier: 5.569A pdb=" N ASP D 29 " --> pdb=" O MET D 84 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'D' and resid 151 through 154 removed outlier: 6.471A pdb=" N HIS D 115 " --> pdb=" O VAL D 166 " (cutoff:3.500A) removed outlier: 4.486A pdb=" N THR D 168 " --> pdb=" O ARG D 113 " (cutoff:3.500A) removed outlier: 6.596A pdb=" N ARG D 113 " --> pdb=" O THR D 168 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'D' and resid 145 through 147 Processing sheet with id=AC1, first strand: chain 'D' and resid 265 through 270 removed outlier: 6.599A pdb=" N ALA D 299 " --> pdb=" O ILE D 342 " (cutoff:3.500A) removed outlier: 7.624A pdb=" N MET D 344 " --> pdb=" O ALA D 299 " (cutoff:3.500A) removed outlier: 5.938A pdb=" N ILE D 301 " --> pdb=" O MET D 344 " (cutoff:3.500A) removed outlier: 7.744A pdb=" N ALA D 346 " --> pdb=" O ILE D 301 " (cutoff:3.500A) removed outlier: 6.774A pdb=" N ILE D 303 " --> pdb=" O ALA D 346 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'D' and resid 538 through 542 removed outlier: 6.573A pdb=" N ASN D 538 " --> pdb=" O VAL D 573 " (cutoff:3.500A) removed outlier: 7.443A pdb=" N PHE D 575 " --> pdb=" O ASN D 538 " (cutoff:3.500A) removed outlier: 6.284A pdb=" N ILE D 540 " --> pdb=" O PHE D 575 " (cutoff:3.500A) removed outlier: 6.475A pdb=" N CYS D 572 " --> pdb=" O PHE D 618 " (cutoff:3.500A) removed outlier: 7.674A pdb=" N ILE D 620 " --> pdb=" O CYS D 572 " (cutoff:3.500A) removed outlier: 6.135A pdb=" N LEU D 574 " --> pdb=" O ILE D 620 " (cutoff:3.500A) removed outlier: 7.772A pdb=" N ALA D 622 " --> pdb=" O LEU D 574 " (cutoff:3.500A) removed outlier: 6.590A pdb=" N PHE D 576 " --> pdb=" O ALA D 622 " (cutoff:3.500A) removed outlier: 6.839A pdb=" N GLY D 513 " --> pdb=" O GLN D 641 " (cutoff:3.500A) removed outlier: 7.895A pdb=" N ILE D 643 " --> pdb=" O GLY D 513 " (cutoff:3.500A) removed outlier: 6.248A pdb=" N LEU D 515 " --> pdb=" O ILE D 643 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'E' and resid 25 through 30 removed outlier: 7.479A pdb=" N ILE E 82 " --> pdb=" O ARG E 25 " (cutoff:3.500A) removed outlier: 6.203A pdb=" N ILE E 27 " --> pdb=" O ILE E 82 " (cutoff:3.500A) removed outlier: 7.182A pdb=" N MET E 84 " --> pdb=" O ILE E 27 " (cutoff:3.500A) removed outlier: 5.569A pdb=" N ASP E 29 " --> pdb=" O MET E 84 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'E' and resid 151 through 154 removed outlier: 6.472A pdb=" N HIS E 115 " --> pdb=" O VAL E 166 " (cutoff:3.500A) removed outlier: 4.486A pdb=" N THR E 168 " --> pdb=" O ARG E 113 " (cutoff:3.500A) removed outlier: 6.596A pdb=" N ARG E 113 " --> pdb=" O THR E 168 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'E' and resid 145 through 147 Processing sheet with id=AC6, first strand: chain 'E' and resid 265 through 270 removed outlier: 6.599A pdb=" N ALA E 299 " --> pdb=" O ILE E 342 " (cutoff:3.500A) removed outlier: 7.623A pdb=" N MET E 344 " --> pdb=" O ALA E 299 " (cutoff:3.500A) removed outlier: 5.937A pdb=" N ILE E 301 " --> pdb=" O MET E 344 " (cutoff:3.500A) removed outlier: 7.743A pdb=" N ALA E 346 " --> pdb=" O ILE E 301 " (cutoff:3.500A) removed outlier: 6.774A pdb=" N ILE E 303 " --> pdb=" O ALA E 346 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'E' and resid 538 through 542 removed outlier: 6.573A pdb=" N ASN E 538 " --> pdb=" O VAL E 573 " (cutoff:3.500A) removed outlier: 7.442A pdb=" N PHE E 575 " --> pdb=" O ASN E 538 " (cutoff:3.500A) removed outlier: 6.284A pdb=" N ILE E 540 " --> pdb=" O PHE E 575 " (cutoff:3.500A) removed outlier: 6.474A pdb=" N CYS E 572 " --> pdb=" O PHE E 618 " (cutoff:3.500A) removed outlier: 7.673A pdb=" N ILE E 620 " --> pdb=" O CYS E 572 " (cutoff:3.500A) removed outlier: 6.135A pdb=" N LEU E 574 " --> pdb=" O ILE E 620 " (cutoff:3.500A) removed outlier: 7.772A pdb=" N ALA E 622 " --> pdb=" O LEU E 574 " (cutoff:3.500A) removed outlier: 6.590A pdb=" N PHE E 576 " --> pdb=" O ALA E 622 " (cutoff:3.500A) removed outlier: 6.839A pdb=" N GLY E 513 " --> pdb=" O GLN E 641 " (cutoff:3.500A) removed outlier: 7.895A pdb=" N ILE E 643 " --> pdb=" O GLY E 513 " (cutoff:3.500A) removed outlier: 6.248A pdb=" N LEU E 515 " --> pdb=" O ILE E 643 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'F' and resid 25 through 30 removed outlier: 7.478A pdb=" N ILE F 82 " --> pdb=" O ARG F 25 " (cutoff:3.500A) removed outlier: 6.203A pdb=" N ILE F 27 " --> pdb=" O ILE F 82 " (cutoff:3.500A) removed outlier: 7.183A pdb=" N MET F 84 " --> pdb=" O ILE F 27 " (cutoff:3.500A) removed outlier: 5.568A pdb=" N ASP F 29 " --> pdb=" O MET F 84 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'F' and resid 151 through 154 removed outlier: 6.472A pdb=" N HIS F 115 " --> pdb=" O VAL F 166 " (cutoff:3.500A) removed outlier: 4.486A pdb=" N THR F 168 " --> pdb=" O ARG F 113 " (cutoff:3.500A) removed outlier: 6.597A pdb=" N ARG F 113 " --> pdb=" O THR F 168 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'F' and resid 145 through 147 Processing sheet with id=AD2, first strand: chain 'F' and resid 265 through 270 removed outlier: 6.599A pdb=" N ALA F 299 " --> pdb=" O ILE F 342 " (cutoff:3.500A) removed outlier: 7.624A pdb=" N MET F 344 " --> pdb=" O ALA F 299 " (cutoff:3.500A) removed outlier: 5.937A pdb=" N ILE F 301 " --> pdb=" O MET F 344 " (cutoff:3.500A) removed outlier: 7.744A pdb=" N ALA F 346 " --> pdb=" O ILE F 301 " (cutoff:3.500A) removed outlier: 6.773A pdb=" N ILE F 303 " --> pdb=" O ALA F 346 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'F' and resid 538 through 542 removed outlier: 6.573A pdb=" N ASN F 538 " --> pdb=" O VAL F 573 " (cutoff:3.500A) removed outlier: 7.442A pdb=" N PHE F 575 " --> pdb=" O ASN F 538 " (cutoff:3.500A) removed outlier: 6.284A pdb=" N ILE F 540 " --> pdb=" O PHE F 575 " (cutoff:3.500A) removed outlier: 6.475A pdb=" N CYS F 572 " --> pdb=" O PHE F 618 " (cutoff:3.500A) removed outlier: 7.674A pdb=" N ILE F 620 " --> pdb=" O CYS F 572 " (cutoff:3.500A) removed outlier: 6.135A pdb=" N LEU F 574 " --> pdb=" O ILE F 620 " (cutoff:3.500A) removed outlier: 7.772A pdb=" N ALA F 622 " --> pdb=" O LEU F 574 " (cutoff:3.500A) removed outlier: 6.589A pdb=" N PHE F 576 " --> pdb=" O ALA F 622 " (cutoff:3.500A) removed outlier: 6.839A pdb=" N GLY F 513 " --> pdb=" O GLN F 641 " (cutoff:3.500A) removed outlier: 7.895A pdb=" N ILE F 643 " --> pdb=" O GLY F 513 " (cutoff:3.500A) removed outlier: 6.249A pdb=" N LEU F 515 " --> pdb=" O ILE F 643 " (cutoff:3.500A) 1683 hydrogen bonds defined for protein. 4716 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 9.78 Time building geometry restraints manager: 3.67 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.35: 12156 1.35 - 1.47: 7157 1.47 - 1.59: 16602 1.59 - 1.71: 37 1.71 - 1.83: 300 Bond restraints: 36252 Sorted by residual: bond pdb=" C10 Y6Y A 903 " pdb=" S Y6Y A 903 " ideal model delta sigma weight residual 1.774 1.594 0.180 2.00e-02 2.50e+03 8.14e+01 bond pdb=" C10 Y6Y B 903 " pdb=" S Y6Y B 903 " ideal model delta sigma weight residual 1.774 1.594 0.180 2.00e-02 2.50e+03 8.12e+01 bond pdb=" C10 Y6Y F 903 " pdb=" S Y6Y F 903 " ideal model delta sigma weight residual 1.774 1.594 0.180 2.00e-02 2.50e+03 8.07e+01 bond pdb=" C10 Y6Y D 903 " pdb=" S Y6Y D 903 " ideal model delta sigma weight residual 1.774 1.594 0.180 2.00e-02 2.50e+03 8.06e+01 bond pdb=" C10 Y6Y E 903 " pdb=" S Y6Y E 903 " ideal model delta sigma weight residual 1.774 1.595 0.179 2.00e-02 2.50e+03 8.04e+01 ... (remaining 36247 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.32: 48628 3.32 - 6.64: 326 6.64 - 9.96: 60 9.96 - 13.28: 6 13.28 - 16.60: 12 Bond angle restraints: 49032 Sorted by residual: angle pdb=" CB ARG C 225 " pdb=" CG ARG C 225 " pdb=" CD ARG C 225 " ideal model delta sigma weight residual 111.30 126.26 -14.96 2.30e+00 1.89e-01 4.23e+01 angle pdb=" CB ARG B 225 " pdb=" CG ARG B 225 " pdb=" CD ARG B 225 " ideal model delta sigma weight residual 111.30 126.24 -14.94 2.30e+00 1.89e-01 4.22e+01 angle pdb=" CB ARG D 225 " pdb=" CG ARG D 225 " pdb=" CD ARG D 225 " ideal model delta sigma weight residual 111.30 126.22 -14.92 2.30e+00 1.89e-01 4.21e+01 angle pdb=" CB ARG E 225 " pdb=" CG ARG E 225 " pdb=" CD ARG E 225 " ideal model delta sigma weight residual 111.30 126.22 -14.92 2.30e+00 1.89e-01 4.21e+01 angle pdb=" CB ARG F 225 " pdb=" CG ARG F 225 " pdb=" CD ARG F 225 " ideal model delta sigma weight residual 111.30 126.22 -14.92 2.30e+00 1.89e-01 4.21e+01 ... (remaining 49027 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.86: 20575 17.86 - 35.72: 1602 35.72 - 53.57: 365 53.57 - 71.43: 150 71.43 - 89.29: 72 Dihedral angle restraints: 22764 sinusoidal: 9882 harmonic: 12882 Sorted by residual: dihedral pdb=" CA GLN C 19 " pdb=" C GLN C 19 " pdb=" N LYS C 20 " pdb=" CA LYS C 20 " ideal model delta harmonic sigma weight residual 180.00 -154.05 -25.95 0 5.00e+00 4.00e-02 2.69e+01 dihedral pdb=" CA GLN A 19 " pdb=" C GLN A 19 " pdb=" N LYS A 20 " pdb=" CA LYS A 20 " ideal model delta harmonic sigma weight residual 180.00 -154.08 -25.92 0 5.00e+00 4.00e-02 2.69e+01 dihedral pdb=" CA GLN B 19 " pdb=" C GLN B 19 " pdb=" N LYS B 20 " pdb=" CA LYS B 20 " ideal model delta harmonic sigma weight residual 180.00 -154.09 -25.91 0 5.00e+00 4.00e-02 2.69e+01 ... (remaining 22761 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.053: 4407 0.053 - 0.106: 887 0.106 - 0.158: 172 0.158 - 0.211: 6 0.211 - 0.264: 6 Chirality restraints: 5478 Sorted by residual: chirality pdb=" C17 Y6Y A 903 " pdb=" C18 Y6Y A 903 " pdb=" C21 Y6Y A 903 " pdb=" S1 Y6Y A 903 " both_signs ideal model delta sigma weight residual False 3.51 3.24 0.26 2.00e-01 2.50e+01 1.74e+00 chirality pdb=" C17 Y6Y F 903 " pdb=" C18 Y6Y F 903 " pdb=" C21 Y6Y F 903 " pdb=" S1 Y6Y F 903 " both_signs ideal model delta sigma weight residual False 3.51 3.25 0.26 2.00e-01 2.50e+01 1.71e+00 chirality pdb=" C17 Y6Y B 903 " pdb=" C18 Y6Y B 903 " pdb=" C21 Y6Y B 903 " pdb=" S1 Y6Y B 903 " both_signs ideal model delta sigma weight residual False 3.51 3.25 0.26 2.00e-01 2.50e+01 1.70e+00 ... (remaining 5475 not shown) Planarity restraints: 6390 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C PRO D 237 " 0.073 5.00e-02 4.00e+02 1.09e-01 1.89e+01 pdb=" N PRO D 238 " -0.188 5.00e-02 4.00e+02 pdb=" CA PRO D 238 " 0.058 5.00e-02 4.00e+02 pdb=" CD PRO D 238 " 0.058 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PRO A 237 " -0.072 5.00e-02 4.00e+02 1.09e-01 1.89e+01 pdb=" N PRO A 238 " 0.188 5.00e-02 4.00e+02 pdb=" CA PRO A 238 " -0.058 5.00e-02 4.00e+02 pdb=" CD PRO A 238 " -0.058 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PRO C 237 " 0.072 5.00e-02 4.00e+02 1.09e-01 1.88e+01 pdb=" N PRO C 238 " -0.188 5.00e-02 4.00e+02 pdb=" CA PRO C 238 " 0.058 5.00e-02 4.00e+02 pdb=" CD PRO C 238 " 0.058 5.00e-02 4.00e+02 ... (remaining 6387 not shown) Histogram of nonbonded interaction distances: 1.99 - 2.57: 288 2.57 - 3.15: 28581 3.15 - 3.73: 56756 3.73 - 4.32: 81802 4.32 - 4.90: 130818 Nonbonded interactions: 298245 Sorted by model distance: nonbonded pdb=" OG1 THR B 252 " pdb="MG MG B 904 " model vdw 1.987 2.170 nonbonded pdb=" OG1 THR E 252 " pdb="MG MG E 904 " model vdw 1.989 2.170 nonbonded pdb=" OG1 THR A 252 " pdb="MG MG A 904 " model vdw 1.996 2.170 nonbonded pdb=" OG1 THR F 252 " pdb="MG MG F 904 " model vdw 1.998 2.170 nonbonded pdb=" OG1 THR C 252 " pdb="MG MG C 904 " model vdw 2.011 2.170 ... (remaining 298240 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.09 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.180 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.020 Construct map_model_manager: 0.030 Extract box with map and model: 0.550 Check model and map are aligned: 0.090 Set scattering table: 0.090 Process input model: 33.990 Find NCS groups from input model: 0.370 Set up NCS constraints: 0.100 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:9.250 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 47.680 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7224 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.180 36252 Z= 0.233 Angle : 0.769 16.598 49032 Z= 0.395 Chirality : 0.045 0.264 5478 Planarity : 0.005 0.109 6390 Dihedral : 15.350 89.289 14400 Min Nonbonded Distance : 1.987 Molprobity Statistics. All-atom Clashscore : 8.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.71 % Favored : 97.29 % Rotamer: Outliers : 1.89 % Allowed : 0.47 % Favored : 97.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.96 (0.13), residues: 4434 helix: 0.96 (0.12), residues: 1962 sheet: 0.52 (0.20), residues: 654 loop : 0.53 (0.15), residues: 1818 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG A 711 TYR 0.011 0.001 TYR C 203 PHE 0.018 0.001 PHE C 742 TRP 0.005 0.001 TRP D 454 HIS 0.004 0.001 HIS A 183 Details of bonding type rmsd covalent geometry : bond 0.00484 (36252) covalent geometry : angle 0.76947 (49032) hydrogen bonds : bond 0.15776 ( 1683) hydrogen bonds : angle 5.62685 ( 4716) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8868 Ramachandran restraints generated. 4434 Oldfield, 0 Emsley, 4434 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8868 Ramachandran restraints generated. 4434 Oldfield, 0 Emsley, 4434 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 303 residues out of total 3822 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 231 time to evaluate : 1.382 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: D 427 MET cc_start: 0.7016 (OUTLIER) cc_final: 0.6588 (mmm) outliers start: 72 outliers final: 5 residues processed: 283 average time/residue: 1.0539 time to fit residues: 336.0393 Evaluate side-chains 150 residues out of total 3822 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 144 time to evaluate : 1.297 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 427 MET Chi-restraints excluded: chain B residue 427 MET Chi-restraints excluded: chain C residue 427 MET Chi-restraints excluded: chain D residue 427 MET Chi-restraints excluded: chain E residue 427 MET Chi-restraints excluded: chain F residue 427 MET Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 444 random chunks: chunk 432 optimal weight: 0.0970 chunk 197 optimal weight: 0.9990 chunk 388 optimal weight: 7.9990 chunk 215 optimal weight: 0.7980 chunk 20 optimal weight: 0.7980 chunk 132 optimal weight: 9.9990 chunk 261 optimal weight: 6.9990 chunk 248 optimal weight: 5.9990 chunk 207 optimal weight: 2.9990 chunk 401 optimal weight: 6.9990 chunk 424 optimal weight: 4.9990 overall best weight: 1.1382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 115 HIS B 115 HIS B 406 HIS C 115 HIS ** C 337 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 115 HIS D 226 HIS E 115 HIS E 406 HIS F 115 HIS Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3815 r_free = 0.3815 target = 0.099960 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3100 r_free = 0.3100 target = 0.059367 restraints weight = 75704.633| |-----------------------------------------------------------------------------| r_work (start): 0.2983 rms_B_bonded: 2.81 r_work: 0.2810 rms_B_bonded: 3.33 restraints_weight: 0.5000 r_work (final): 0.2810 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8376 moved from start: 0.1353 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 36252 Z= 0.138 Angle : 0.559 6.610 49032 Z= 0.295 Chirality : 0.044 0.162 5478 Planarity : 0.005 0.081 6390 Dihedral : 11.000 77.734 5466 Min Nonbonded Distance : 2.000 Molprobity Statistics. All-atom Clashscore : 6.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.10 % Favored : 97.90 % Rotamer: Outliers : 0.63 % Allowed : 5.97 % Favored : 93.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.39 (0.13), residues: 4434 helix: 1.21 (0.11), residues: 2034 sheet: 0.76 (0.20), residues: 624 loop : 0.87 (0.15), residues: 1776 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG E 338 TYR 0.007 0.001 TYR F 755 PHE 0.009 0.001 PHE B 563 TRP 0.006 0.001 TRP D 454 HIS 0.008 0.001 HIS F 115 Details of bonding type rmsd covalent geometry : bond 0.00311 (36252) covalent geometry : angle 0.55856 (49032) hydrogen bonds : bond 0.04136 ( 1683) hydrogen bonds : angle 4.45541 ( 4716) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8868 Ramachandran restraints generated. 4434 Oldfield, 0 Emsley, 4434 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8868 Ramachandran restraints generated. 4434 Oldfield, 0 Emsley, 4434 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 163 residues out of total 3822 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 139 time to evaluate : 1.312 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 199 ASN cc_start: 0.8907 (m-40) cc_final: 0.8524 (p0) REVERT: C 158 MET cc_start: 0.7072 (OUTLIER) cc_final: 0.6810 (pp-130) REVERT: D 158 MET cc_start: 0.6919 (OUTLIER) cc_final: 0.6677 (pp-130) outliers start: 24 outliers final: 7 residues processed: 147 average time/residue: 0.7700 time to fit residues: 133.8786 Evaluate side-chains 143 residues out of total 3822 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 134 time to evaluate : 1.322 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 115 HIS Chi-restraints excluded: chain C residue 115 HIS Chi-restraints excluded: chain C residue 158 MET Chi-restraints excluded: chain D residue 115 HIS Chi-restraints excluded: chain D residue 158 MET Chi-restraints excluded: chain D residue 198 LEU Chi-restraints excluded: chain E residue 115 HIS Chi-restraints excluded: chain F residue 115 HIS Chi-restraints excluded: chain F residue 198 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 444 random chunks: chunk 305 optimal weight: 0.0370 chunk 287 optimal weight: 10.0000 chunk 87 optimal weight: 7.9990 chunk 159 optimal weight: 7.9990 chunk 441 optimal weight: 6.9990 chunk 394 optimal weight: 2.9990 chunk 89 optimal weight: 5.9990 chunk 370 optimal weight: 10.0000 chunk 225 optimal weight: 0.0470 chunk 193 optimal weight: 0.1980 chunk 79 optimal weight: 6.9990 overall best weight: 1.8560 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 115 HIS B 115 HIS B 183 HIS ** B 337 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 115 HIS C 183 HIS ** C 337 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 115 HIS D 183 HIS E 115 HIS E 183 HIS ** E 337 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 115 HIS F 183 HIS F 226 HIS Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3790 r_free = 0.3790 target = 0.098451 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.3064 r_free = 0.3064 target = 0.057740 restraints weight = 75640.150| |-----------------------------------------------------------------------------| r_work (start): 0.2947 rms_B_bonded: 2.79 r_work: 0.2773 rms_B_bonded: 3.28 restraints_weight: 0.5000 r_work: 0.2632 rms_B_bonded: 4.94 restraints_weight: 0.2500 r_work (final): 0.2632 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8510 moved from start: 0.1656 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 36252 Z= 0.156 Angle : 0.514 6.556 49032 Z= 0.272 Chirality : 0.044 0.155 5478 Planarity : 0.004 0.070 6390 Dihedral : 10.892 74.341 5448 Min Nonbonded Distance : 1.942 Molprobity Statistics. All-atom Clashscore : 5.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.32 % Favored : 97.68 % Rotamer: Outliers : 0.81 % Allowed : 6.89 % Favored : 92.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.56 (0.13), residues: 4434 helix: 1.35 (0.12), residues: 2046 sheet: 0.77 (0.20), residues: 624 loop : 0.99 (0.16), residues: 1764 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG F 338 TYR 0.016 0.001 TYR C 138 PHE 0.010 0.001 PHE D 302 TRP 0.006 0.001 TRP D 454 HIS 0.012 0.002 HIS D 115 Details of bonding type rmsd covalent geometry : bond 0.00366 (36252) covalent geometry : angle 0.51447 (49032) hydrogen bonds : bond 0.04071 ( 1683) hydrogen bonds : angle 4.29214 ( 4716) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8868 Ramachandran restraints generated. 4434 Oldfield, 0 Emsley, 4434 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8868 Ramachandran restraints generated. 4434 Oldfield, 0 Emsley, 4434 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 172 residues out of total 3822 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 141 time to evaluate : 1.434 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 46 MET cc_start: 0.6484 (mpt) cc_final: 0.6278 (mpt) REVERT: B 199 ASN cc_start: 0.8925 (m110) cc_final: 0.8530 (p0) REVERT: C 158 MET cc_start: 0.7021 (OUTLIER) cc_final: 0.6744 (pp-130) REVERT: D 158 MET cc_start: 0.6843 (OUTLIER) cc_final: 0.6583 (pp-130) REVERT: F 427 MET cc_start: 0.8528 (mmm) cc_final: 0.8312 (mmm) outliers start: 31 outliers final: 8 residues processed: 156 average time/residue: 0.7276 time to fit residues: 135.8950 Evaluate side-chains 140 residues out of total 3822 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 130 time to evaluate : 1.367 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 115 HIS Chi-restraints excluded: chain A residue 508 MET Chi-restraints excluded: chain C residue 158 MET Chi-restraints excluded: chain C residue 198 LEU Chi-restraints excluded: chain C residue 403 THR Chi-restraints excluded: chain D residue 158 MET Chi-restraints excluded: chain D residue 198 LEU Chi-restraints excluded: chain F residue 46 MET Chi-restraints excluded: chain F residue 198 LEU Chi-restraints excluded: chain F residue 403 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 444 random chunks: chunk 15 optimal weight: 20.0000 chunk 261 optimal weight: 6.9990 chunk 86 optimal weight: 20.0000 chunk 170 optimal weight: 0.6980 chunk 395 optimal weight: 5.9990 chunk 188 optimal weight: 2.9990 chunk 201 optimal weight: 2.9990 chunk 306 optimal weight: 10.0000 chunk 300 optimal weight: 20.0000 chunk 330 optimal weight: 4.9990 chunk 293 optimal weight: 6.9990 overall best weight: 3.5388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 115 HIS ** A 337 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 337 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 337 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 337 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 558 ASN ** F 337 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3752 r_free = 0.3752 target = 0.095751 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 70)----------------| | r_work = 0.3001 r_free = 0.3001 target = 0.055031 restraints weight = 76156.695| |-----------------------------------------------------------------------------| r_work (start): 0.2890 rms_B_bonded: 2.77 r_work: 0.2711 rms_B_bonded: 3.25 restraints_weight: 0.5000 r_work: 0.2569 rms_B_bonded: 4.93 restraints_weight: 0.2500 r_work (final): 0.2569 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8564 moved from start: 0.2068 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.054 36252 Z= 0.256 Angle : 0.565 7.193 49032 Z= 0.296 Chirality : 0.046 0.173 5478 Planarity : 0.005 0.066 6390 Dihedral : 11.059 74.657 5448 Min Nonbonded Distance : 1.872 Molprobity Statistics. All-atom Clashscore : 6.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.14 % Favored : 97.86 % Rotamer: Outliers : 0.55 % Allowed : 7.81 % Favored : 91.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.51 (0.13), residues: 4434 helix: 1.25 (0.11), residues: 2082 sheet: 0.73 (0.20), residues: 624 loop : 1.04 (0.16), residues: 1728 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG D 86 TYR 0.006 0.001 TYR A 755 PHE 0.011 0.002 PHE E 452 TRP 0.009 0.002 TRP D 454 HIS 0.012 0.002 HIS F 115 Details of bonding type rmsd covalent geometry : bond 0.00612 (36252) covalent geometry : angle 0.56533 (49032) hydrogen bonds : bond 0.04538 ( 1683) hydrogen bonds : angle 4.33527 ( 4716) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8868 Ramachandran restraints generated. 4434 Oldfield, 0 Emsley, 4434 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8868 Ramachandran restraints generated. 4434 Oldfield, 0 Emsley, 4434 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 159 residues out of total 3822 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 138 time to evaluate : 1.335 Fit side-chains revert: symmetry clash REVERT: A 46 MET cc_start: 0.6337 (mpt) cc_final: 0.6111 (mpt) REVERT: A 158 MET cc_start: 0.7536 (pmm) cc_final: 0.7281 (ppp) REVERT: A 403 THR cc_start: 0.9291 (OUTLIER) cc_final: 0.9040 (p) REVERT: B 158 MET cc_start: 0.7567 (pmm) cc_final: 0.7303 (ppp) REVERT: B 199 ASN cc_start: 0.8926 (m110) cc_final: 0.8538 (p0) REVERT: B 508 MET cc_start: 0.9047 (OUTLIER) cc_final: 0.8825 (tmm) REVERT: C 46 MET cc_start: 0.7137 (OUTLIER) cc_final: 0.6762 (mpp) REVERT: C 158 MET cc_start: 0.7315 (OUTLIER) cc_final: 0.7060 (pp-130) REVERT: D 158 MET cc_start: 0.6928 (OUTLIER) cc_final: 0.6696 (pp-130) REVERT: E 158 MET cc_start: 0.7430 (pmm) cc_final: 0.7216 (ppp) REVERT: E 199 ASN cc_start: 0.8962 (m-40) cc_final: 0.8544 (p0) REVERT: E 508 MET cc_start: 0.9087 (ttt) cc_final: 0.8842 (tmm) outliers start: 21 outliers final: 8 residues processed: 148 average time/residue: 0.6814 time to fit residues: 121.2634 Evaluate side-chains 143 residues out of total 3822 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 130 time to evaluate : 1.197 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 403 THR Chi-restraints excluded: chain A residue 508 MET Chi-restraints excluded: chain B residue 508 MET Chi-restraints excluded: chain C residue 46 MET Chi-restraints excluded: chain C residue 158 MET Chi-restraints excluded: chain C residue 198 LEU Chi-restraints excluded: chain C residue 403 THR Chi-restraints excluded: chain D residue 158 MET Chi-restraints excluded: chain D residue 198 LEU Chi-restraints excluded: chain F residue 46 MET Chi-restraints excluded: chain F residue 198 LEU Chi-restraints excluded: chain F residue 336 LYS Chi-restraints excluded: chain F residue 403 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 444 random chunks: chunk 22 optimal weight: 0.9990 chunk 82 optimal weight: 4.9990 chunk 380 optimal weight: 30.0000 chunk 400 optimal weight: 5.9990 chunk 41 optimal weight: 3.9990 chunk 345 optimal weight: 2.9990 chunk 271 optimal weight: 2.9990 chunk 59 optimal weight: 0.5980 chunk 252 optimal weight: 0.8980 chunk 374 optimal weight: 10.0000 chunk 332 optimal weight: 3.9990 overall best weight: 1.6986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 115 HIS ** A 337 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 90 ASN B 115 HIS ** B 337 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 115 HIS ** C 337 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 115 HIS ** D 337 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 90 ASN E 115 HIS ** E 337 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 115 HIS ** F 337 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3765 r_free = 0.3765 target = 0.096554 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3028 r_free = 0.3028 target = 0.056052 restraints weight = 75691.085| |-----------------------------------------------------------------------------| r_work (start): 0.2915 rms_B_bonded: 2.80 r_work: 0.2738 rms_B_bonded: 3.31 restraints_weight: 0.5000 r_work: 0.2598 rms_B_bonded: 4.97 restraints_weight: 0.2500 r_work (final): 0.2598 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8523 moved from start: 0.2151 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 36252 Z= 0.143 Angle : 0.489 7.507 49032 Z= 0.257 Chirality : 0.043 0.154 5478 Planarity : 0.004 0.060 6390 Dihedral : 10.616 76.204 5448 Min Nonbonded Distance : 1.949 Molprobity Statistics. All-atom Clashscore : 5.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.19 % Favored : 97.81 % Rotamer: Outliers : 0.58 % Allowed : 8.33 % Favored : 91.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.65 (0.13), residues: 4434 helix: 1.42 (0.11), residues: 2082 sheet: 0.71 (0.21), residues: 624 loop : 1.08 (0.16), residues: 1728 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG F 93 TYR 0.006 0.001 TYR A 755 PHE 0.010 0.001 PHE C 152 TRP 0.007 0.001 TRP D 454 HIS 0.007 0.001 HIS D 115 Details of bonding type rmsd covalent geometry : bond 0.00337 (36252) covalent geometry : angle 0.48866 (49032) hydrogen bonds : bond 0.03666 ( 1683) hydrogen bonds : angle 4.12852 ( 4716) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8868 Ramachandran restraints generated. 4434 Oldfield, 0 Emsley, 4434 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8868 Ramachandran restraints generated. 4434 Oldfield, 0 Emsley, 4434 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 151 residues out of total 3822 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 129 time to evaluate : 1.372 Fit side-chains revert: symmetry clash REVERT: A 46 MET cc_start: 0.6336 (mpt) cc_final: 0.6098 (mpt) REVERT: B 199 ASN cc_start: 0.8914 (m110) cc_final: 0.8511 (p0) REVERT: B 508 MET cc_start: 0.9042 (ttt) cc_final: 0.8783 (tmm) REVERT: C 46 MET cc_start: 0.7093 (OUTLIER) cc_final: 0.6719 (mtp) REVERT: C 158 MET cc_start: 0.7347 (OUTLIER) cc_final: 0.7036 (ppp) REVERT: E 199 ASN cc_start: 0.8960 (m-40) cc_final: 0.8535 (p0) REVERT: E 508 MET cc_start: 0.9087 (ttt) cc_final: 0.8790 (tmm) outliers start: 22 outliers final: 10 residues processed: 142 average time/residue: 0.7084 time to fit residues: 120.3605 Evaluate side-chains 138 residues out of total 3822 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 126 time to evaluate : 1.299 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 115 HIS Chi-restraints excluded: chain B residue 115 HIS Chi-restraints excluded: chain C residue 46 MET Chi-restraints excluded: chain C residue 115 HIS Chi-restraints excluded: chain C residue 158 MET Chi-restraints excluded: chain C residue 198 LEU Chi-restraints excluded: chain D residue 115 HIS Chi-restraints excluded: chain D residue 198 LEU Chi-restraints excluded: chain E residue 115 HIS Chi-restraints excluded: chain F residue 46 MET Chi-restraints excluded: chain F residue 115 HIS Chi-restraints excluded: chain F residue 198 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 444 random chunks: chunk 324 optimal weight: 6.9990 chunk 333 optimal weight: 0.7980 chunk 100 optimal weight: 6.9990 chunk 153 optimal weight: 10.0000 chunk 336 optimal weight: 5.9990 chunk 430 optimal weight: 2.9990 chunk 83 optimal weight: 30.0000 chunk 109 optimal weight: 5.9990 chunk 114 optimal weight: 5.9990 chunk 327 optimal weight: 5.9990 chunk 189 optimal weight: 1.9990 overall best weight: 3.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 337 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 115 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 337 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 115 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 337 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 115 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 337 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 115 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 337 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 115 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 337 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3746 r_free = 0.3746 target = 0.095344 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.2995 r_free = 0.2995 target = 0.054715 restraints weight = 76031.154| |-----------------------------------------------------------------------------| r_work (start): 0.2886 rms_B_bonded: 2.75 r_work: 0.2707 rms_B_bonded: 3.26 restraints_weight: 0.5000 r_work: 0.2566 rms_B_bonded: 4.92 restraints_weight: 0.2500 r_work (final): 0.2566 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8568 moved from start: 0.2312 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.043 36252 Z= 0.262 Angle : 0.549 8.994 49032 Z= 0.287 Chirality : 0.046 0.147 5478 Planarity : 0.004 0.059 6390 Dihedral : 10.639 76.285 5448 Min Nonbonded Distance : 1.900 Molprobity Statistics. All-atom Clashscore : 5.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.14 % Favored : 97.86 % Rotamer: Outliers : 0.74 % Allowed : 8.62 % Favored : 90.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.57 (0.13), residues: 4434 helix: 1.35 (0.11), residues: 2082 sheet: 0.74 (0.21), residues: 624 loop : 1.01 (0.16), residues: 1728 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG F 93 TYR 0.025 0.001 TYR B 173 PHE 0.012 0.002 PHE D 131 TRP 0.008 0.001 TRP D 454 HIS 0.011 0.002 HIS B 115 Details of bonding type rmsd covalent geometry : bond 0.00626 (36252) covalent geometry : angle 0.54931 (49032) hydrogen bonds : bond 0.04324 ( 1683) hydrogen bonds : angle 4.26244 ( 4716) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8868 Ramachandran restraints generated. 4434 Oldfield, 0 Emsley, 4434 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8868 Ramachandran restraints generated. 4434 Oldfield, 0 Emsley, 4434 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 164 residues out of total 3822 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 136 time to evaluate : 1.336 Fit side-chains REVERT: A 46 MET cc_start: 0.6380 (mpt) cc_final: 0.6116 (mpt) REVERT: A 158 MET cc_start: 0.7344 (pmm) cc_final: 0.7111 (ppp) REVERT: B 199 ASN cc_start: 0.8914 (m110) cc_final: 0.8511 (p0) REVERT: B 508 MET cc_start: 0.9067 (ttt) cc_final: 0.8828 (tmm) REVERT: B 757 MET cc_start: 0.8502 (OUTLIER) cc_final: 0.8041 (tmm) REVERT: C 46 MET cc_start: 0.7134 (OUTLIER) cc_final: 0.6756 (mpp) REVERT: C 158 MET cc_start: 0.7535 (OUTLIER) cc_final: 0.7266 (ppp) REVERT: C 199 ASN cc_start: 0.8947 (m-40) cc_final: 0.8573 (p0) REVERT: E 199 ASN cc_start: 0.8954 (m-40) cc_final: 0.8520 (p0) REVERT: E 508 MET cc_start: 0.9102 (ttt) cc_final: 0.8834 (tmm) REVERT: F 199 ASN cc_start: 0.8958 (m-40) cc_final: 0.8565 (p0) outliers start: 28 outliers final: 9 residues processed: 153 average time/residue: 0.7345 time to fit residues: 134.0746 Evaluate side-chains 143 residues out of total 3822 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 131 time to evaluate : 1.191 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 508 MET Chi-restraints excluded: chain B residue 757 MET Chi-restraints excluded: chain C residue 46 MET Chi-restraints excluded: chain C residue 151 ILE Chi-restraints excluded: chain C residue 158 MET Chi-restraints excluded: chain C residue 198 LEU Chi-restraints excluded: chain C residue 403 THR Chi-restraints excluded: chain D residue 198 LEU Chi-restraints excluded: chain F residue 46 MET Chi-restraints excluded: chain F residue 151 ILE Chi-restraints excluded: chain F residue 198 LEU Chi-restraints excluded: chain F residue 403 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 444 random chunks: chunk 353 optimal weight: 5.9990 chunk 184 optimal weight: 0.9990 chunk 233 optimal weight: 30.0000 chunk 375 optimal weight: 9.9990 chunk 20 optimal weight: 1.9990 chunk 7 optimal weight: 0.0070 chunk 299 optimal weight: 9.9990 chunk 238 optimal weight: 20.0000 chunk 46 optimal weight: 0.5980 chunk 249 optimal weight: 4.9990 chunk 64 optimal weight: 0.9990 overall best weight: 0.9204 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 337 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 337 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 337 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 337 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 337 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 337 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3768 r_free = 0.3768 target = 0.096653 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3029 r_free = 0.3029 target = 0.056138 restraints weight = 75841.881| |-----------------------------------------------------------------------------| r_work (start): 0.2922 rms_B_bonded: 2.79 r_work: 0.2746 rms_B_bonded: 3.30 restraints_weight: 0.5000 r_work: 0.2603 rms_B_bonded: 4.97 restraints_weight: 0.2500 r_work (final): 0.2603 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8533 moved from start: 0.2345 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 36252 Z= 0.110 Angle : 0.482 8.855 49032 Z= 0.252 Chirality : 0.043 0.155 5478 Planarity : 0.004 0.056 6390 Dihedral : 10.227 79.083 5448 Min Nonbonded Distance : 1.967 Molprobity Statistics. All-atom Clashscore : 5.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.14 % Favored : 97.86 % Rotamer: Outliers : 0.74 % Allowed : 8.91 % Favored : 90.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.72 (0.13), residues: 4434 helix: 1.54 (0.12), residues: 2082 sheet: 0.48 (0.20), residues: 660 loop : 1.16 (0.16), residues: 1692 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 599 TYR 0.021 0.001 TYR B 173 PHE 0.010 0.001 PHE B 363 TRP 0.007 0.001 TRP D 454 HIS 0.010 0.001 HIS A 115 Details of bonding type rmsd covalent geometry : bond 0.00257 (36252) covalent geometry : angle 0.48157 (49032) hydrogen bonds : bond 0.03402 ( 1683) hydrogen bonds : angle 4.05938 ( 4716) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8868 Ramachandran restraints generated. 4434 Oldfield, 0 Emsley, 4434 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8868 Ramachandran restraints generated. 4434 Oldfield, 0 Emsley, 4434 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 160 residues out of total 3822 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 132 time to evaluate : 1.379 Fit side-chains revert: symmetry clash REVERT: A 46 MET cc_start: 0.6320 (mpt) cc_final: 0.6070 (mpt) REVERT: A 225 ARG cc_start: 0.9004 (OUTLIER) cc_final: 0.8791 (mmm-85) REVERT: B 158 MET cc_start: 0.7748 (pmm) cc_final: 0.7361 (ppp) REVERT: B 199 ASN cc_start: 0.8919 (m110) cc_final: 0.8498 (p0) REVERT: B 225 ARG cc_start: 0.9107 (OUTLIER) cc_final: 0.8810 (mmm-85) REVERT: B 508 MET cc_start: 0.9086 (ttt) cc_final: 0.8796 (tmm) REVERT: B 701 GLU cc_start: 0.8738 (OUTLIER) cc_final: 0.8522 (tt0) REVERT: C 46 MET cc_start: 0.7098 (OUTLIER) cc_final: 0.6734 (mtp) REVERT: C 158 MET cc_start: 0.7566 (OUTLIER) cc_final: 0.7314 (ppp) REVERT: E 158 MET cc_start: 0.7508 (pmm) cc_final: 0.7118 (ppp) REVERT: E 199 ASN cc_start: 0.8980 (m-40) cc_final: 0.8542 (p0) REVERT: E 508 MET cc_start: 0.9112 (ttt) cc_final: 0.8792 (tmm) REVERT: F 158 MET cc_start: 0.7410 (pmm) cc_final: 0.7162 (ppp) outliers start: 28 outliers final: 10 residues processed: 151 average time/residue: 0.7275 time to fit residues: 131.1602 Evaluate side-chains 145 residues out of total 3822 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 130 time to evaluate : 1.262 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 225 ARG Chi-restraints excluded: chain A residue 508 MET Chi-restraints excluded: chain B residue 173 TYR Chi-restraints excluded: chain B residue 225 ARG Chi-restraints excluded: chain B residue 701 GLU Chi-restraints excluded: chain C residue 46 MET Chi-restraints excluded: chain C residue 158 MET Chi-restraints excluded: chain C residue 198 LEU Chi-restraints excluded: chain C residue 403 THR Chi-restraints excluded: chain D residue 198 LEU Chi-restraints excluded: chain E residue 198 LEU Chi-restraints excluded: chain E residue 225 ARG Chi-restraints excluded: chain F residue 46 MET Chi-restraints excluded: chain F residue 198 LEU Chi-restraints excluded: chain F residue 403 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 444 random chunks: chunk 55 optimal weight: 3.9990 chunk 60 optimal weight: 0.7980 chunk 276 optimal weight: 4.9990 chunk 435 optimal weight: 0.8980 chunk 402 optimal weight: 9.9990 chunk 431 optimal weight: 1.9990 chunk 146 optimal weight: 10.0000 chunk 277 optimal weight: 1.9990 chunk 134 optimal weight: 1.9990 chunk 17 optimal weight: 30.0000 chunk 376 optimal weight: 50.0000 overall best weight: 1.5386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 115 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 337 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 337 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 337 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 337 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 337 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 337 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3763 r_free = 0.3763 target = 0.096318 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3031 r_free = 0.3031 target = 0.056057 restraints weight = 75899.977| |-----------------------------------------------------------------------------| r_work (start): 0.2919 rms_B_bonded: 2.78 r_work: 0.2741 rms_B_bonded: 3.28 restraints_weight: 0.5000 r_work: 0.2600 rms_B_bonded: 4.96 restraints_weight: 0.2500 r_work (final): 0.2600 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8547 moved from start: 0.2432 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 36252 Z= 0.137 Angle : 0.491 9.864 49032 Z= 0.255 Chirality : 0.043 0.151 5478 Planarity : 0.004 0.054 6390 Dihedral : 10.057 80.925 5448 Min Nonbonded Distance : 1.955 Molprobity Statistics. All-atom Clashscore : 5.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.23 % Favored : 97.77 % Rotamer: Outliers : 0.66 % Allowed : 9.17 % Favored : 90.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.77 (0.13), residues: 4434 helix: 1.59 (0.12), residues: 2082 sheet: 0.50 (0.20), residues: 660 loop : 1.17 (0.16), residues: 1692 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG F 93 TYR 0.023 0.001 TYR E 173 PHE 0.009 0.001 PHE C 758 TRP 0.008 0.001 TRP D 454 HIS 0.012 0.001 HIS F 115 Details of bonding type rmsd covalent geometry : bond 0.00325 (36252) covalent geometry : angle 0.49145 (49032) hydrogen bonds : bond 0.03479 ( 1683) hydrogen bonds : angle 4.02463 ( 4716) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8868 Ramachandran restraints generated. 4434 Oldfield, 0 Emsley, 4434 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8868 Ramachandran restraints generated. 4434 Oldfield, 0 Emsley, 4434 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 158 residues out of total 3822 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 133 time to evaluate : 1.140 Fit side-chains revert: symmetry clash REVERT: A 46 MET cc_start: 0.6378 (mpt) cc_final: 0.6135 (mpt) REVERT: A 317 HIS cc_start: 0.8113 (m90) cc_final: 0.7871 (t-90) REVERT: B 158 MET cc_start: 0.7600 (pmm) cc_final: 0.7207 (ppp) REVERT: B 199 ASN cc_start: 0.8910 (m110) cc_final: 0.8483 (p0) REVERT: B 225 ARG cc_start: 0.9070 (OUTLIER) cc_final: 0.8773 (mmm-85) REVERT: B 508 MET cc_start: 0.9099 (ttt) cc_final: 0.8775 (tmm) REVERT: B 701 GLU cc_start: 0.8721 (OUTLIER) cc_final: 0.8498 (tt0) REVERT: B 757 MET cc_start: 0.8526 (OUTLIER) cc_final: 0.8050 (tmm) REVERT: C 46 MET cc_start: 0.7023 (OUTLIER) cc_final: 0.6654 (mtp) REVERT: C 158 MET cc_start: 0.7520 (OUTLIER) cc_final: 0.7307 (ppp) REVERT: C 199 ASN cc_start: 0.8935 (m-40) cc_final: 0.8564 (p0) REVERT: D 225 ARG cc_start: 0.8965 (OUTLIER) cc_final: 0.8755 (mmm-85) REVERT: E 158 MET cc_start: 0.7612 (pmm) cc_final: 0.7288 (ppp) REVERT: E 199 ASN cc_start: 0.8954 (m-40) cc_final: 0.8515 (p0) REVERT: E 225 ARG cc_start: 0.9072 (OUTLIER) cc_final: 0.8770 (mmm-85) REVERT: E 508 MET cc_start: 0.9130 (ttt) cc_final: 0.8800 (tmm) REVERT: F 158 MET cc_start: 0.7511 (pmm) cc_final: 0.7283 (ppp) REVERT: F 199 ASN cc_start: 0.8944 (m-40) cc_final: 0.8553 (p0) outliers start: 25 outliers final: 11 residues processed: 151 average time/residue: 0.7246 time to fit residues: 130.9107 Evaluate side-chains 150 residues out of total 3822 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 132 time to evaluate : 1.157 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 225 ARG Chi-restraints excluded: chain A residue 508 MET Chi-restraints excluded: chain B residue 173 TYR Chi-restraints excluded: chain B residue 225 ARG Chi-restraints excluded: chain B residue 701 GLU Chi-restraints excluded: chain B residue 757 MET Chi-restraints excluded: chain C residue 46 MET Chi-restraints excluded: chain C residue 158 MET Chi-restraints excluded: chain C residue 198 LEU Chi-restraints excluded: chain C residue 403 THR Chi-restraints excluded: chain D residue 198 LEU Chi-restraints excluded: chain D residue 225 ARG Chi-restraints excluded: chain E residue 198 LEU Chi-restraints excluded: chain E residue 225 ARG Chi-restraints excluded: chain F residue 46 MET Chi-restraints excluded: chain F residue 151 ILE Chi-restraints excluded: chain F residue 198 LEU Chi-restraints excluded: chain F residue 403 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 444 random chunks: chunk 379 optimal weight: 6.9990 chunk 195 optimal weight: 3.9990 chunk 394 optimal weight: 3.9990 chunk 368 optimal weight: 8.9990 chunk 405 optimal weight: 4.9990 chunk 349 optimal weight: 1.9990 chunk 155 optimal weight: 20.0000 chunk 158 optimal weight: 8.9990 chunk 316 optimal weight: 0.7980 chunk 51 optimal weight: 4.9990 chunk 121 optimal weight: 3.9990 overall best weight: 2.9588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 115 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 337 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 115 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 337 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 337 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 337 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 337 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 337 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3749 r_free = 0.3749 target = 0.095449 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3003 r_free = 0.3003 target = 0.054939 restraints weight = 76009.194| |-----------------------------------------------------------------------------| r_work (start): 0.2893 rms_B_bonded: 2.77 r_work: 0.2716 rms_B_bonded: 3.27 restraints_weight: 0.5000 r_work: 0.2571 rms_B_bonded: 4.94 restraints_weight: 0.2500 r_work (final): 0.2571 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8566 moved from start: 0.2497 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.044 36252 Z= 0.224 Angle : 0.535 10.160 49032 Z= 0.276 Chirality : 0.045 0.182 5478 Planarity : 0.004 0.055 6390 Dihedral : 10.093 80.328 5448 Min Nonbonded Distance : 1.913 Molprobity Statistics. All-atom Clashscore : 6.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.28 % Favored : 97.72 % Rotamer: Outliers : 0.87 % Allowed : 9.17 % Favored : 89.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.68 (0.13), residues: 4434 helix: 1.50 (0.11), residues: 2082 sheet: 0.50 (0.20), residues: 660 loop : 1.13 (0.16), residues: 1692 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 377 TYR 0.026 0.001 TYR E 173 PHE 0.010 0.001 PHE E 452 TRP 0.007 0.001 TRP D 454 HIS 0.012 0.002 HIS F 115 Details of bonding type rmsd covalent geometry : bond 0.00536 (36252) covalent geometry : angle 0.53477 (49032) hydrogen bonds : bond 0.03932 ( 1683) hydrogen bonds : angle 4.12780 ( 4716) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8868 Ramachandran restraints generated. 4434 Oldfield, 0 Emsley, 4434 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8868 Ramachandran restraints generated. 4434 Oldfield, 0 Emsley, 4434 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 167 residues out of total 3822 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 134 time to evaluate : 1.177 Fit side-chains revert: symmetry clash REVERT: A 46 MET cc_start: 0.6351 (mpt) cc_final: 0.6065 (mpt) REVERT: A 225 ARG cc_start: 0.8993 (OUTLIER) cc_final: 0.8747 (mmm-85) REVERT: A 317 HIS cc_start: 0.8158 (m90) cc_final: 0.7816 (t-90) REVERT: B 158 MET cc_start: 0.7620 (pmm) cc_final: 0.7261 (ppp) REVERT: B 199 ASN cc_start: 0.8921 (m110) cc_final: 0.8491 (p0) REVERT: B 225 ARG cc_start: 0.9098 (OUTLIER) cc_final: 0.8804 (mmm-85) REVERT: B 508 MET cc_start: 0.9105 (ttt) cc_final: 0.8814 (tmm) REVERT: B 701 GLU cc_start: 0.8754 (OUTLIER) cc_final: 0.8546 (tt0) REVERT: B 757 MET cc_start: 0.8513 (OUTLIER) cc_final: 0.8046 (tmm) REVERT: C 46 MET cc_start: 0.7070 (OUTLIER) cc_final: 0.6708 (mtp) REVERT: C 158 MET cc_start: 0.7606 (OUTLIER) cc_final: 0.7404 (ppp) REVERT: C 199 ASN cc_start: 0.8944 (m-40) cc_final: 0.8570 (p0) REVERT: C 317 HIS cc_start: 0.8264 (m90) cc_final: 0.7878 (t-90) REVERT: D 199 ASN cc_start: 0.8870 (m-40) cc_final: 0.8396 (p0) REVERT: D 225 ARG cc_start: 0.9002 (OUTLIER) cc_final: 0.8790 (mmm-85) REVERT: E 158 MET cc_start: 0.7552 (pmm) cc_final: 0.7004 (pp-130) REVERT: E 199 ASN cc_start: 0.8962 (m-40) cc_final: 0.8523 (p0) REVERT: E 225 ARG cc_start: 0.9099 (OUTLIER) cc_final: 0.8800 (mmm-85) REVERT: E 508 MET cc_start: 0.9134 (OUTLIER) cc_final: 0.8791 (tmm) REVERT: F 158 MET cc_start: 0.7534 (pmm) cc_final: 0.7317 (ppp) REVERT: F 199 ASN cc_start: 0.8953 (m-40) cc_final: 0.8562 (p0) outliers start: 33 outliers final: 11 residues processed: 155 average time/residue: 0.7219 time to fit residues: 133.6085 Evaluate side-chains 154 residues out of total 3822 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 134 time to evaluate : 1.329 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 123 VAL Chi-restraints excluded: chain A residue 225 ARG Chi-restraints excluded: chain B residue 173 TYR Chi-restraints excluded: chain B residue 225 ARG Chi-restraints excluded: chain B residue 701 GLU Chi-restraints excluded: chain B residue 757 MET Chi-restraints excluded: chain C residue 46 MET Chi-restraints excluded: chain C residue 158 MET Chi-restraints excluded: chain C residue 198 LEU Chi-restraints excluded: chain C residue 225 ARG Chi-restraints excluded: chain C residue 403 THR Chi-restraints excluded: chain D residue 198 LEU Chi-restraints excluded: chain D residue 225 ARG Chi-restraints excluded: chain E residue 173 TYR Chi-restraints excluded: chain E residue 198 LEU Chi-restraints excluded: chain E residue 225 ARG Chi-restraints excluded: chain E residue 508 MET Chi-restraints excluded: chain F residue 46 MET Chi-restraints excluded: chain F residue 198 LEU Chi-restraints excluded: chain F residue 403 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 444 random chunks: chunk 239 optimal weight: 6.9990 chunk 318 optimal weight: 7.9990 chunk 169 optimal weight: 3.9990 chunk 329 optimal weight: 0.6980 chunk 2 optimal weight: 30.0000 chunk 197 optimal weight: 0.8980 chunk 323 optimal weight: 4.9990 chunk 77 optimal weight: 0.0060 chunk 32 optimal weight: 4.9990 chunk 195 optimal weight: 1.9990 chunk 208 optimal weight: 2.9990 overall best weight: 1.3200 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 115 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 337 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 115 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 337 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 337 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 337 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 337 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 337 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3764 r_free = 0.3764 target = 0.096372 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 74)----------------| | r_work = 0.3031 r_free = 0.3031 target = 0.056047 restraints weight = 76107.769| |-----------------------------------------------------------------------------| r_work (start): 0.2920 rms_B_bonded: 2.79 r_work: 0.2742 rms_B_bonded: 3.29 restraints_weight: 0.5000 r_work: 0.2601 rms_B_bonded: 4.98 restraints_weight: 0.2500 r_work (final): 0.2601 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8549 moved from start: 0.2541 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 36252 Z= 0.125 Angle : 0.493 10.672 49032 Z= 0.256 Chirality : 0.043 0.152 5478 Planarity : 0.004 0.053 6390 Dihedral : 9.772 81.594 5448 Min Nonbonded Distance : 1.961 Molprobity Statistics. All-atom Clashscore : 5.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.21 % Favored : 97.79 % Rotamer: Outliers : 0.63 % Allowed : 9.41 % Favored : 89.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.80 (0.13), residues: 4434 helix: 1.64 (0.12), residues: 2064 sheet: 0.67 (0.20), residues: 642 loop : 1.08 (0.16), residues: 1728 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 599 TYR 0.024 0.001 TYR E 173 PHE 0.010 0.001 PHE E 363 TRP 0.007 0.001 TRP D 454 HIS 0.012 0.001 HIS F 115 Details of bonding type rmsd covalent geometry : bond 0.00295 (36252) covalent geometry : angle 0.49272 (49032) hydrogen bonds : bond 0.03412 ( 1683) hydrogen bonds : angle 4.01389 ( 4716) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8868 Ramachandran restraints generated. 4434 Oldfield, 0 Emsley, 4434 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8868 Ramachandran restraints generated. 4434 Oldfield, 0 Emsley, 4434 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 159 residues out of total 3822 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 135 time to evaluate : 1.540 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 46 MET cc_start: 0.6305 (mpt) cc_final: 0.6042 (mpt) REVERT: A 317 HIS cc_start: 0.8193 (m90) cc_final: 0.7799 (t-90) REVERT: B 158 MET cc_start: 0.7649 (pmm) cc_final: 0.7304 (ppp) REVERT: B 199 ASN cc_start: 0.8899 (m110) cc_final: 0.8478 (p0) REVERT: B 225 ARG cc_start: 0.9086 (OUTLIER) cc_final: 0.8852 (mmm-85) REVERT: B 508 MET cc_start: 0.9094 (ttt) cc_final: 0.8763 (tmm) REVERT: B 701 GLU cc_start: 0.8736 (OUTLIER) cc_final: 0.8515 (tt0) REVERT: B 757 MET cc_start: 0.8523 (OUTLIER) cc_final: 0.8063 (tmm) REVERT: C 46 MET cc_start: 0.7102 (OUTLIER) cc_final: 0.6734 (mtp) REVERT: C 199 ASN cc_start: 0.8935 (m-40) cc_final: 0.8565 (p0) REVERT: C 317 HIS cc_start: 0.8261 (m90) cc_final: 0.7652 (t-90) REVERT: D 317 HIS cc_start: 0.8190 (m90) cc_final: 0.7739 (t70) REVERT: E 158 MET cc_start: 0.7569 (pmm) cc_final: 0.7015 (pp-130) REVERT: E 199 ASN cc_start: 0.8956 (m-40) cc_final: 0.8506 (p0) REVERT: E 225 ARG cc_start: 0.9088 (OUTLIER) cc_final: 0.8844 (mmm-85) REVERT: E 508 MET cc_start: 0.9120 (OUTLIER) cc_final: 0.8785 (tmm) REVERT: F 84 MET cc_start: 0.7360 (OUTLIER) cc_final: 0.6695 (tmt) REVERT: F 158 MET cc_start: 0.7573 (pmm) cc_final: 0.7363 (ppp) REVERT: F 199 ASN cc_start: 0.8939 (m-40) cc_final: 0.8552 (p0) outliers start: 24 outliers final: 15 residues processed: 149 average time/residue: 0.7627 time to fit residues: 135.7297 Evaluate side-chains 156 residues out of total 3822 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 134 time to evaluate : 1.401 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 123 VAL Chi-restraints excluded: chain A residue 225 ARG Chi-restraints excluded: chain A residue 508 MET Chi-restraints excluded: chain B residue 173 TYR Chi-restraints excluded: chain B residue 225 ARG Chi-restraints excluded: chain B residue 701 GLU Chi-restraints excluded: chain B residue 757 MET Chi-restraints excluded: chain C residue 46 MET Chi-restraints excluded: chain C residue 198 LEU Chi-restraints excluded: chain C residue 225 ARG Chi-restraints excluded: chain C residue 403 THR Chi-restraints excluded: chain D residue 198 LEU Chi-restraints excluded: chain D residue 225 ARG Chi-restraints excluded: chain E residue 123 VAL Chi-restraints excluded: chain E residue 173 TYR Chi-restraints excluded: chain E residue 198 LEU Chi-restraints excluded: chain E residue 225 ARG Chi-restraints excluded: chain E residue 508 MET Chi-restraints excluded: chain F residue 46 MET Chi-restraints excluded: chain F residue 84 MET Chi-restraints excluded: chain F residue 198 LEU Chi-restraints excluded: chain F residue 403 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 444 random chunks: chunk 260 optimal weight: 4.9990 chunk 140 optimal weight: 0.8980 chunk 402 optimal weight: 9.9990 chunk 412 optimal weight: 5.9990 chunk 20 optimal weight: 1.9990 chunk 216 optimal weight: 7.9990 chunk 86 optimal weight: 0.0000 chunk 37 optimal weight: 7.9990 chunk 139 optimal weight: 0.8980 chunk 318 optimal weight: 6.9990 chunk 430 optimal weight: 3.9990 overall best weight: 1.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 115 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 337 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 115 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 337 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 337 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 337 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 337 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 337 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3763 r_free = 0.3763 target = 0.096248 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3023 r_free = 0.3023 target = 0.055734 restraints weight = 75685.013| |-----------------------------------------------------------------------------| r_work (start): 0.2915 rms_B_bonded: 2.80 r_work: 0.2740 rms_B_bonded: 3.28 restraints_weight: 0.5000 r_work: 0.2599 rms_B_bonded: 4.95 restraints_weight: 0.2500 r_work (final): 0.2599 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8548 moved from start: 0.2600 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 36252 Z= 0.137 Angle : 0.502 12.220 49032 Z= 0.258 Chirality : 0.043 0.149 5478 Planarity : 0.004 0.053 6390 Dihedral : 9.635 83.286 5448 Min Nonbonded Distance : 1.952 Molprobity Statistics. All-atom Clashscore : 5.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.26 % Favored : 97.74 % Rotamer: Outliers : 0.76 % Allowed : 9.28 % Favored : 89.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.82 (0.13), residues: 4434 helix: 1.66 (0.12), residues: 2064 sheet: 0.53 (0.20), residues: 660 loop : 1.17 (0.16), residues: 1710 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG C 159 TYR 0.024 0.001 TYR E 173 PHE 0.009 0.001 PHE D 302 TRP 0.007 0.001 TRP D 454 HIS 0.012 0.001 HIS F 115 Details of bonding type rmsd covalent geometry : bond 0.00327 (36252) covalent geometry : angle 0.50167 (49032) hydrogen bonds : bond 0.03450 ( 1683) hydrogen bonds : angle 3.99703 ( 4716) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 17306.56 seconds wall clock time: 293 minutes 21.14 seconds (17601.14 seconds total)